/*-
 * #%L
 * Utility classes for BoneJ1 plugins
 * %%
 * Copyright (C) 2015 - 2023 Michael Doube, BoneJ developers
 * %%
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
 * 
 * 1. Redistributions of source code must retain the above copyright notice,
 *    this list of conditions and the following disclaimer.
 * 2. Redistributions in binary form must reproduce the above copyright notice,
 *    this list of conditions and the following disclaimer in the documentation
 *    and/or other materials provided with the distribution.
 * 
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
 * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
 * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
 * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
 * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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 * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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 * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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 * #L%
 */


package org.bonej.util;

import ij.ImagePlus;
import ij.plugin.filter.PlugInFilter;
import sc.fiji.skeletonize3D.Skeletonize3D_;

/**
 * Utility methods for working with the {@link Skeletonize3D_} plugin
 *
 * @author Michael Doube
 * @author Mark Hiner
 */
public final class SkeletonUtils {

	private static final PlugInFilter skeletoniser = new Skeletonize3D_();

	private SkeletonUtils() {}

	/**
	 * Gets a medial axis skeleton from a binary imp using a topology-preserving
	 * iterative algorithm
	 *
	 * @param imp input image
	 * @return skeletonised image
	 */

	public static ImagePlus getSkeleton(final ImagePlus imp) {
		// TODO Duplicate so that ROIs don't affect the result (side effect of
		// duplicate())
		final ImagePlus skeleton = imp.duplicate();

		skeletoniser.setup("", skeleton);
		skeletoniser.run(null);

		skeleton.setCalibration(imp.getCalibration());
		skeleton.setTitle("Skeleton of " + imp.getTitle());
		return skeleton;
	}
}
